Raw goat milk collected at 11 Andalusian dairy plants was used to individually manufacture cheeses without starter culture addition. Microbial groups were monitored during ripening for 60 days. A total of 1442 lactic acid bacteria (LAB) isolates randomly chosen were identified by molecular methods. Counts of mesophilic LAB exceeded 9 log cfu g−1 on day 1 and decreased 0.5 log units during ripening whereas counts of lactobacilli and leuconostocs increased and those of enterococci remained constant. Thirty-three LAB species belonging to eight different genera were isolated, with higher biodiversity on day 1 (26 species) than on day 60 (20 species). Structural genes coding for nisin, lacticin 481, lactococcin B, six plantaricins and five enterocins were detected in LAB isolates. The information obtained on the technological properties of selected isolates may be useful in developing specific starters for goat milk cheeses, capable of maintaining their distinctive sensory characteristics.